Dicarbonyls simulation

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This page describes the optional dicarbonyls chemistry mechanism as implemented in GEOS-Chem.

Contents

Overview

Brief description

From Fu et al [2008]:

We use the Master Chemistry Mechanism version 3.1 (MCMv3.1) [Saunders et al., 2003; Bloss et al., 2005] as principal guide for the VOC chemistry leading to glyoxal and methylglyoxal formation. Primary VOC precursors include isoalkanes, alkenes, acetylene, aromatics, isoprene, monoterpenes, acetone, methylbutenol (2-methyl-3-buten-2-ol), glycolaldehyde, and hydroxyacetone. The latter two are secondary products of VOC oxidation but are also emitted directly by biofuel use and open biomass burning. Glyoxal and methylglyoxal are themselves also emitted directly from these two sources [McDonald et al., 2000; Hays et al., 2002]. Primary anthropogenic emissions of glyoxal and methylglyoxal are small [Environmental Protection Agency, 2004; Volkamer et al., 2005b] and are not considered here.
GEOS-Chem includes a detailed O3-NOx-VOC-aerosol chemical mechanism [Horowitz et al., 1998; Bey et al., 2001; Martin et al., 2003; Park et al., 2006]. ... Fu et al. [2007] added to the model the chemistry of ethylene and xylenes For this work, we further updated the photochemical mechanisms of isoprene, propene, acetylene, glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone based on MCMv3.1 and Jet Propulsion Laboratory (JPL) [2006]. The quantum yield for acetone photolysis is updated to be dependent on both temperature and pressure, based on Blitz et al. [2004]. We also added parameterized dicarbonyl production from benzene, toluene, xylenes, monoterpenes, and methylbutenol.

Authors and collaborators

Dicarbonyls simulation user groups

User Group Personnel Projects
Peking University Tzung-May Fu ...
Univeristy of Minnesoata Dylan Millet ...
Colorado State University Colette Heald ...

--Bob Y. 16:10, 26 February 2010 (EST)

Input files

As described in Chapter 2.3: Downloading the GEOS-Chem Run Directories in the GEOS-Chem Online User's Guide, you can use a Git Clone command to download run directories for the dicarbonyls simulation.

The command will take the form: 

   git clone git://git.as.harvard.edu/bmy/GEOS-Chem-rundirs/DIR-OPTION LOCAL-DIR-NAME

LOCAL-DIR-NAME is the name under which the run directory will be stored in your disk space.

DIR-OPTION may be one of the following:

DIR-OPTION Description
2x2.5/geos4/dicarbonyls 2 x 2.5 GEOS-4 fullchem w/ dicarbonyls option
2x2.5/geos5/dicarbonyls 2 x 2.5 GEOS-5 fullchem w/ dicarbonyls option
4x5/geos4/dicarbonyls 4 x 5 GEOS-4 fullchem w/ dicarbonyls option
4x5/geos5/dicarbonyls 4 x 5 GEOS-5 fullchem w/ dicarbonyls option
4x5/merra/dicarbonyls 4 x 5 MERRA fullchem w/ dicarbonyls option

NOTES:

  1. We no longer distribute the run directories via TARBALL (*.tar.gz) files.
  2. At present, not all run directories have current restart files. We would like to ask dicarbonyl simulation users to consider sending restart files from your simulations.
  3. The GEOS-Chem Support Team is not responsible for the scientific content of the dicarbonyl simulation. We will make sure that your updates get added to the standard code, but we are not responsible for validating the dicarbonyl simulation against observations.

--Bob Y. 16:36, 14 February 2011 (EST)

References

  1. Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation, J. Geophys. Res., 106, 23,073-23,096, 2001. PDF
  2. Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, and M. P. Chipperfield, Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm, Geophys. Res. Lett., 31, L06111, doi:10.1029/2003GL018793, 2004.
  3. Bloss, C., et al., Development of detailed chemical mechanism (MCMv3.1) for the atmospheric oxidation of aromatic hydrocarbons, Atmos. Chem. Phys., 5, 641–664, 2005.
  4. Environmental Protection Agency, 1999 National emissions inventory version 3.0, Environmental Protection Agency, Washington, D.C., 2004. Link
  5. Horowitz, L.W., J. Liang, G.M. Gardner, and D.J. Jacob, Export of reactive nitrogen from North America during summertime, J. Geophys. Res., 103, 13,451-13,476, 1998. PDF
  6. Fu, T.-M., D. J. Jacob, P. I. Palmer, K. Chance, Y. X. Wang, B. Barletta, D. R. Blake, J. C. Stanton, M. J. Pilling, Space-based formaldehyde measurements as constraints on volatile organic compound emissions in East and South Asia, J. Geophys. Res., 112, D06312, doi:10.1029/2006JD007853, 2007. PDF
  7. Fu, T.-M., D.J. Jacob, and C.L. Heald, Aqueous-phase reactive uptake of dicarbonyls as a source of organic aerosol over eastern North America, Atmos. Environ., 43, 1,814-1,822, 2009.PDF
  8. Hays, M. D., C. D. Geron, K. J. Linna, N. D. Smith, and J. J. Schauer, Speciation of gas-phase and fine particle emissions from burning of foliar fuels, Environ. Sci. Technol., 36(11), 2281–2295, doi:10.1021/es0111683, 2002.
  9. Jet Propulsion Laboratory (JPL), Chemical Kinetics and PhotochemicalData for Use in Atmospheric Studies, Evaluation Number 15, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, 2006.
  10. Martin, R.V., D.J. Jacob, R.M. Yantosca, M. Chin, and P. Ginoux, Global and Regional Decreases in Tropospheric Oxidants from Photochemical Effects of Aerosols, J. Geophys. Res., 108(D3), 4097, doi:10.1029/2002JD002622. PDF
  11. McDonald, J. D., B. Zielinska, E. M. Fujita, J. C. Sagebiel, J. C. Chow, and J. G. Watson, Fine particle and gaseous emission rates from residential wood combustion, Environ. Sci. Technol., 34(11), 2080–2091, doi:10.1021/es9909632, 2000.
  12. Park, R. J., D. J. Jacob, N. Kumar, and R. M. Yantosca, Regional visibility statistics in the United States: Natural and transboundary pollution influences, and implications for the Regional Haze Rule, Atmos. Environ., 40(28), 5405-5423, 2006. PDF
  13. Saunders, S. M., M. E. Jenkin, R. G. Derwen, and M. J. Pilling, Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): Tropospheric degradation of non-aromatic volatile organic compounds, Atmos. Chem. Phys., 3, 161–180, 2003.
  14. Volkamer, R., L. T. Molina, M. J. Molina, T. Shirley, and W. H. Brune, DOAS measurement of glyoxal as an indicator for fast VOC chemistry in urban air,Geophys. Res. Lett., 32, L08806, doi:10.1029/2005GL022616, 2005.

--Bob Y. 15:57, 26 February 2010 (EST)

Previous issues now resolved

Out-of-bounds error in SOAG_LIGGIO_DIFF

This update was tested in the 1-month benchmark simulation v9-01-03n and approved on 08 Jun 2012.

There was an out-of-bounds error in SOAG_LIGGIO_DIFF. Here is the solution:

Claire Carouge wrote:

In fact, in SOAG_LIGGIO_DIFF (carbon_mod.f), there is a loop over LLTROP. It's the maximum number of levels for the tropopause. But in the loop we use JLOP indexes which are 0 outside the actual tropopause.
So the fix is to add the line: 
           ! JLOP equal 0 if we're not in the tropopause. (ccc,10/16/09)
           IF ( JLOOP == 0 ) CYCLE
after line 1224: 
           ! Get 1-D index
           JLOOP   = JLOP( I, J, L )
There is the same kind of loop in SOAM_LIGGIO_DIFF just after. You should add the same fix.

--Ccarouge 12:54, 16 October 2009 (EDT)
--Bob Y. 13:57, 18 February 2011 (EST)

NL parameter needs to be increased

This update was tested in the 1-month benchmark simulation v9-01-03n and approved on 08 Jun 2012.

Colette Heald reported that the NL parameter in FAST-J header file jv_mie.h needs to be updated to 2000 in order to prevent the dicarbonyl simulation from crashing. The fix is as follows: 

!-----------------------------------------------------------------------
!     NL=1500 was too small for dicarbonyls, so we upped it to 1500.
!     Uncomment this line to restore the previous definition (phs, 10/9/09)
!      PARAMETER (NL=1500, N__=2*NL, M__=4)
!-----------------------------------------------------------------------
      PARAMETER (NL=2000, N__=2*NL, M__=4)

--Bob Y. 13:57, 18 February 2011 (EST)

Input file issues

Dylan Millet wrote:

I found some problems with the standard v8-2-1 code and specific run directories for running dicarbonyl simulations, which lead to mysterious and cryptic run death. globchem.dat has an extra line under the HNO3 emission and before the NO2 drydep (line 2170 needs to be deleted). I also ran into other problems which I traced to read-in errors with jv_spec.dat (...).
--Dbm 00:00, 12 October 2009 (EDT)

The problem that Dylan described above has now been corrected. We now provide several run directories (grouped by met field type and horizontal resolution) for the GEOS-Chem dicarbonyls simulation. For instructions how to download these, please see the input files section above.

--Bob Y. 13:57, 18 February 2011 (EST)

Out-of-bounds error in drydep_mod.f

If you are running the 75-tracer dicarbonyl simulation with a version of GEOS-Chem prior to v9-01-01, then make sure that you set this parameter in drydep_mod.f: 

     INTEGER, PARAMETER   :: MAXDEP    = 51

Otherwise you will get an out-of-bounds error and the code will die in routine DEPVEL (in drydep_mod.f). 

forrtl: severe (408): fort: (2): Subscript #1 of the array NTRAIND has value 51 
        which is greater than the upper bound of 50

Image              PC                Routine            Line        Source              
geos               00000000007661F2  drydep_mod_mp_ini        3642  drydep_mod.f
geos               00000000009DEEFD  input_mod_mp_read        2377  input_mod.f
geos               00000000009CE975  input_mod_mp_read         281  input_mod.f
geos               0000000000A501BB  MAIN__                    208  main.f

This error was probably introduced when the number of tracers was increased from 73 to 75; somehow the maximum number of dry-depositing species (MAXDEP) was not simultaneously increased. It is now fixed in v9-01-01.

You will also want to make sure you fix these typos in edgar_mod.f.

--Bob Y. 15:59, 14 February 2011 (EST)

Outstanding issues not yet resolved

KPP is not compatible with the dicarbonyls simulation

As of Feb 2010, the files needed to use the KPP solver were not generated for the dicarbonyls chemistry. You can not run the dicarbonyls chemistry with the KPP solver. You have to use SMVGEAR.

If someone is so motivated, one can build the KPP solver files with the dicarbonyls chemistry mechanism on their own.

--Bob Y. 16:20, 26 February 2010 (EST)

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